19-46493902-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020709.3(PNMA8B):c.1564G>T(p.Ala522Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 152,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020709.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNMA8B | ENST00000599531.2 | c.1564G>T | p.Ala522Ser | missense_variant | Exon 1 of 1 | 6 | NM_020709.3 | ENSP00000473036.1 | ||
PNMA8B | ENST00000594749.1 | n.165+1813G>T | intron_variant | Intron 1 of 1 | 5 | |||||
PPP5D1P | ENST00000602017.7 | n.378-12462G>T | intron_variant | Intron 3 of 3 | 3 | |||||
PPP5D1P | ENST00000702671.1 | n.394-12462G>T | intron_variant | Intron 4 of 4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000456 AC: 1AN: 219252Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 120530
GnomAD4 exome Cov.: 36
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1564G>T (p.A522S) alteration is located in exon 1 (coding exon 1) of the PNMAL2 gene. This alteration results from a G to T substitution at nucleotide position 1564, causing the alanine (A) at amino acid position 522 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at